Abstract
study about biological sequences is gaining momentum nowadays. An increasing number of researchers have proposed framework for the implementation of various algorithms for biomolecules sequence alignment and secondary structure prediction. A comparative study can also enhance the results but alignment and prediction algorithms vary widely in terms of both sensitivity and selectivity across different lengths and homologies. The independent benchmarking of these algorithms is rarely performed for siRNA sequences. Sequence alignment and determination of the secondary structure of biomolecules are very important for understanding their functions and behavior. This paper presents the implementation of Nussinov algorithm using Bio-Perl for the study of behavior of siRNA sequences.
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